Phenotyping and genotyping are both essential to identify and classify a probiotic microorganism.

The use of probiotic products, especially for humans, requires an unequivocal taxonomical definition of their microbial content, in order to assign the probiotic effects to well identified and characterized microbial strains. In the absence of this, the labeling of some marketed probiotics may be misleading, both in terms of microbiological contents and possible beneficial effects. Currently, the 'polyphasic taxonomy' based on the integration of phenotypic and genotypic data seems to be the most appropriate approach. In fact, even if phenotypic characters often overlap among genetically different species, the molecular methods alone are frequently not able to establish distinct boundaries among phylogenetically related species. Thus, a valid scheme for the identification of a probiotic strain should be currently based on its morphological, physiological, and biochemical features as well as on aspects of its genetic profile. It is important that the identity of specific probiotic strains appearing on the product label is the result of a carefully selected combination of suitable phenotypic and genotypic analytical methods. Only adoption of such a policy could give the right emphasis to the significance of strain-specificity and thus provide health authorities with accurate tools to better evaluate the health benefits claimed by each probiotic-based product. The most common phenotypic and genotypic methods are briefly reviewed here with the aim of highlighting the suitable techniques which can be used to differentiate among microorganisms of probiotic interest, particularly those claiming beneficial health effects for humans.